Molecular Dynamics Simulation Studies on the Hybridization Events of Surface Immobilized DNA

Abstract

Surfaces functionalized with ssDNAs can be used to uniquely and reversibly bind complimentary DNAs. Such DNA modified materials are used in nanoscale supramolecular assembly, as optical, electrochemical and piezoelectric biosensors. Recognition and recombination pathways of DNA functionalized system are regulated by ssDNA hybridization. We conducted molecular dynamics simulation studies of DNA strands thiolated on the surface and in the presence of duplex and compared their dynamics to the dynamics of the DNA strands in solution. We investigated the optimal ssDNA length, effect of linker type and length to understand the effect of immobilization on subsequent DNA hybridization. Our results indicate that sensitivity and selectivity are directly dependent on the length and sequence of ssDNA strands. The persistence length, folding pathway and time are directly dependent on the hybridization and length of ssDNA. Minimum energy pathways were explored to understand the kinetics of ssDNA folding during the event of hybridization. Simulations suggest that restrained ssDNAs, compared to labile suspensions of free ssDNAs, are more capable of hybridization and hence DNA-based assembly. Our study helps understanding the science associated with the ssDNA hybridization and provides feedback to the associated experiments.